Laboratory mice are frequently used in biomedical studies. Facial expressions of mice provides important data about various issues. For this reason real time tracking of mice provide output to both researcher and software that operate on face image directly. Since body and face of laboratory mice is the same color and mice moves fast, tracking of face of mice is a challenging task. In recent years, methods that uses artificial neural networks provide effective solutions to problems such as classification, decision making and object recognition due to their ability to abstract training from data. In this study, a method based on deep learning is proposed for real time tracking of face of mice and successful results are obtained. Our studies are still going on in order to improve our results obtained using a limited dataset.